The Bioconductor project

BioC

Packages analyse all kinds of Genomic data (>800)
Compulsory documentation (vignettes) for each package
6-month release cycle
Course Materials
Example data and workflows
Common, re-usable framework and functionality
Available Support

Advantages of R

Open-source
Cross-platform
Reproducibility
Access to existing visualisation / statistical tools
Flexibility
Visualisation and interactivity

Recent Press

NYT

Recent Press

Nature

Support for R

Online forums
Local user groups
Documentation via ? or help.start()

RStudio

Rstudio is a free environment for R
Convenient menus to access scripts, display plots
Still need to use command-line to get things done
Developed by some of the leading R programmers

R recap

R can do simple numerical calculations

2  + 2

## [1] 4

sqrt(25)

## [1] 5

Here, sqrt is a function and the number 25 was used as an argument to the function. Functions can have multiple arguments

variables

We can save the result of a computation as a variable using the assignment operator <-

x <- sqrt(25)
x + 5

## [1] 10

y <- x +5
y

## [1] 10

vectors

A vector can be used to combine multiple values. The resulting object is indexed and particular values can be queried using the [] operator

vec <- c(1,2,3,6)
vec[1]

## [1] 1

vectors

Calculations can be performed on vectors

vec*2

## [1]  2  4  6 12

mean(vec)

## [1] 3

sum(vec)

## [1] 12

Data frames

These can be used to represent familiar tabular (row and column) data

df <- data.frame(A = c(1,2,3,6), B = c(7,8,10,12))
df

##   A  B
## 1 1  7
## 2 2  8
## 3 3 10
## 4 6 12

Data frames

Don’t need the same data type in each column

df <- data.frame(A = c(1,2,3,6), 
                 B = month.name[c(7,8,10,12)])
df

##   A        B
## 1 1     July
## 2 2   August
## 3 3  October
## 4 6 December

Data frame

We can subset data frames using the [], but can specify row and column indices

df[1,2]

## [1] July
## Levels: August December July October

df[2,1]

## [1] 2

Data frame

df[1,]

##   A    B
## 1 1 July

df[,2]

## [1] July     August   October  December
## Levels: August December July October

Or leave the row or column index blank to get all rows and columns respectively